relWarps returning an error

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newsboys6
2013-09-30
2013-09-30
  • newsboys6
    newsboys6
    2013-09-30

    Hello!

    I am working with landmarks collected from bivalve mollusks using imageJ to digitize positions. When I read data into R and place them in a 3 dimensional array and try to calculate relative warps, I get an error message.

    I have tried troubleshooting the problem by both running the command before and after I perform a procrusts superimpostion but based on the way relWarps works it really shouldnt matter (I think, at least based on the code...). I can plot all points just fine and run a superimposition perfectly so I do not think that there is anything wrong with my data (but I could be wrong). I have also tried to run relWarps on my system with some of the built in data (ape skulls landmarks I believe it was) and got the exact same error.

    I am runing R using Rkward for Linux (Xubuntu).

    Any help is greatly appreciated. Thanks in advance.

    Below, see pasted my R-session:

    chione <- read.csv(file="chlm.csv")
    chlm <- array(NA, dim=c(14,2,20))
    chlm[,1,] <- chione[,1]
    chlm[,2,] <- chione[,2]
    library(Morpho)
    wrps <- relWarps(chlm)

    Error in bePCs %*% diag(rep(diaginv, 3)) : non-conformable arguments
    Calls: relWarps

    sessionInfo()
    R version 3.0.2 (2013-09-25)
    Platform: i686-pc-linux-gnu (32-bit)

    locale:
    [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
    [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
    [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
    [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
    [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8

    attached base packages:
    [1] parallel stats graphics grDevices utils datasets methods
    [8] base

    other attached packages:
    [1] Morpho_0.25-1 doParallel_1.0.3 iterators_1.0.6 Matrix_1.0-14
    [5] lattice_0.20-23 foreach_1.4.1 rgl_0.93.952 rkward_0.6.1

    loaded via a namespace (and not attached):
    [1] codetools_0.2-8 colorRamps_2.3 grid_3.0.2 MASS_7.3-29
    [5] tools_3.0.2 yaImpute_1.0-19

     
  • zarquon
    zarquon
    2013-09-30

    Hi,

    thank you for reporting this bug.
    I assume you use 2D data... I only tested with 3D and did not recognize the flaw. As you use linux. I attached the source package of the latest development snapshot. Please update "rgl" before installing it by issueing

        install.packages("rgl")
    

    because the ltatest version is required.

    To install this package open a terminal, navigate to the download folder and issue

       R CMD INSTALL Morpho_0.99.tar.gz
    

    (on debian/ubuntu you will need to install r-base-dev on your machine)

    All the best
    Stefan

     
    Last edit: zarquon 2013-09-30
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